These standards ensure consistent formatting across all NeuroWiki pages. Follow them exactly.
# Top-Level Heading (Page Title)
## Section Heading
### Subsection Heading
#### Deep Subsection
**Bold** for emphasis
*Italic* for book titles, foreign words
***Bold Italic*** for strong emphasis
All references go in the YAML frontmatter:
---
title: "Page Title"
description: "Description here"
refs:
smith2023:
authors: "Smith J, Jones M"
title: "Paper Title"
journal: "Nature Neuroscience"
year: 2023
pmid: "12345678"
doe2024:
authors: "Doe J, et al."
title: "Another Paper"
journal: "Lancet Neurology"
year: 2024
doi: "10.1234/example"
---
Required fields: title, year
At least one of: pmid, doi, url
Use [@citekey] in the body:
Alzheimer's disease affects millions[@smith2023].
Novel treatments show promise[@doe2024].
The sync pipeline converts these to numbered footnotes.
Always hyperlink DOIs and PMIDs:
1. [Smith et al., Amyloid cascade (2023)](https://pubmed.ncbi.nlm.nih.gov/12345678/)
2. [Doe et al., Novel therapy (2024)](https://doi.org/10.1234/example)
Never write: DOI: 10.1234 or PMID: 12345678
Correct format:
[Display Text](/path/to/page)
Examples:
[APP Gene](/entities/app)[Alpha-Synuclein](/proteins/alpha-synuclein)[Alzheimer's Disease](/diseases/alzheimers-disease)Path prefixes:
/entities/ — genes, proteins/diseases/ — diseases/mechanisms/ — pathways/cell-types/ — cell types/treatments/ — therapeutics/clinical-trials/ — trials/researchers/ — scientists/institutions/ — universities, hospitalsRules:
[APP](/entities/app)[the gene](/entities/app)[Display Text](https://example.com)
| Entity | Format | Example |
|---|---|---|
| Gene | "GeneName Gene" | "LRRK2 Gene" |
| Protein | "ProteinName" | "Alpha-Synuclein" |
| Disease | "Disease Name" | "Alzheimer's Disease" |
| Mechanism | "Mechanism Name" | "Amyloid Cascade" |
| Cell Type | "Cell Type Name" | "Microglia" |
| Therapeutic | "Drug Name" | "Donepezil" |
Always use the standard page path:
/entities/gene-name/proteins/protein-name[APP](/entities/app) not [this protein](/entities/app)For pathway visualizations:
Rules:
["double quotes"][1] in body text[text] without a URL[text [more](url) breaks parsing[DOI](https://doi.org/...)| Error | Correction |
|---|---|
[Gene](/genes/app) |
/entities/app (no /genes/) |
PMID: 12345 |
[PMID: 12345](https://pubmed.ncbi.nlm.nih.gov/12345/) |
# Section |
## Section (use >= H2) |
[text](url) (closed parens) |
Before publishing, run:
# Check references
python3 scripts/reference_lint.py --check path/to/page.md
# Check links
python3 scripts/link_fixer.py audit --path path/
# Check markdown
python3 scripts/mermaid_lint.py --check path/to/page.md
| Category | Standard |
|---|---|
| Title | "LRRK2 Gene" |
| Link | [LRRK2](/entities/lrrk2) |
| Ref | [@citekey] in body |
| Heading | ## Section Name |
| Ref link | [PMID](https://pubmed.ncbi.nlm.nih.gov/...) |